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#/*##########################################################################
# Copyright (C) 2004-2014 V.A. Sole, European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
"""
This stack plugin provides filtering and background subtraction methods:
- Savitzky-Golay Filtering (smoothing)
- Deglitch with SNIP 1D Background
- Subtract SNIP 1D Background
- Subtract SNIP 2D Background
- Subtract active curve
"""
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
from PyMca5 import StackPluginBase
from PyMca5.PyMcaGui import SGWindow
from PyMca5.PyMcaGui import SNIPWindow
from PyMca5.PyMcaGui import PyMca_Icons as PyMca_Icons
import numpy
DEBUG = 0
class BackgroundStackPlugin(StackPluginBase.StackPluginBase):
def __init__(self, stackWindow, **kw):
StackPluginBase.DEBUG = DEBUG
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
SGtext = "Replace current stack by a\n"
SGtext += "Savitsky-Golay treated one."
SNIP1Dtext = "Replace current stack by a\n"
SNIP1Dtext += "SNIP1D treated one."
SNIP2Dtext = "Replace current stack by a\n"
SNIP2Dtext += "SNIP2D treated one."
self.methodDict = {}
function = self.replaceStackWithSavitzkyGolayFiltering
info = SGtext
icon = PyMca_Icons.substract
self.methodDict["Savitzky-Golay Filtering"] = [function, info, icon]
function = self.subtract1DSnipBackground
info = SNIP1Dtext
self.methodDict["Subtract SNIP 1D Background"] = [function, info, icon]
function = self.replaceWith1DSnipBackground
info = "Smooth and replace current stack\n"
info += "by its SNIP1D background."
self.methodDict["Deglitch with SNIP 1D Background"] = [function,
info,
PyMca_Icons.smooth]
function = self.subtract2DSnipBackground
info = SNIP2Dtext
self.methodDict["Subtract SNIP 2D Background"] = [function, info, icon]
function = self.subtractActiveCurve
info = "Replace current stack by one in which\nthe active curve has been subtracted"
self.methodDict["Subtract active curve"] = [function, info, icon]
self.__methodKeys = ["Savitzky-Golay Filtering",
"Deglitch with SNIP 1D Background",
"Subtract SNIP 1D Background",
"Subtract SNIP 2D Background",
"Subtract active curve"]
def stackUpdated(self):
self.dialogWidget = None
#Methods implemented by the plugin
def getMethods(self):
return self.__methodKeys
def getMethodToolTip(self, name):
return self.methodDict[name][1]
def getMethodPixmap(self, name):
return self.methodDict[name][2]
def applyMethod(self, name):
return self.methodDict[name][0]()
def replaceStackWithSavitzkyGolayFiltering(self):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve
snipWindow = SGWindow.SGDialog(None,
spectrum, x=x)
snipWindow.graph.setGraphXLabel(info['xlabel'])
snipWindow.graph.setGraphYLabel(info['ylabel'])
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec_()
if ret:
snipParametersDict = snipWindow.getParameters()
snipWindow.close()
function = snipParametersDict['function']
arguments = snipParametersDict['arguments']
stack = self.getStackDataObject()
function(stack, *arguments)
self.setStack(stack)
def subtract1DSnipBackground(self, smooth=False):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
x, spectrum, legend, info = activeCurve
snipWindow = SNIPWindow.SNIPDialog(None,
spectrum, x=x, smooth=smooth)
snipWindow.graph.setGraphXLabel(info['xlabel'])
snipWindow.graph.setGraphYLabel(info['ylabel'])
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec_()
if ret:
snipParametersDict = snipWindow.getParameters()
snipWindow.close()
function = snipParametersDict['function']
arguments = snipParametersDict['arguments']
stack = self.getStackDataObject()
function(stack, *arguments)
self.setStack(stack)
def replaceWith1DSnipBackground(self):
return self.subtract1DSnipBackground(smooth=True)
def subtract2DSnipBackground(self):
imageList = self.getStackROIImagesAndNames()
if imageList is None:
return
imageList, imageNames = imageList
if not len(imageList):
return
snipWindow = SNIPWindow.SNIPDialog(None,
imageList[0] * 1)
#snipWindow.setModal(True)
snipWindow.show()
ret = snipWindow.exec_()
if ret:
snipParametersDict = snipWindow.getParameters()
snipWindow.close()
function = snipParametersDict['function']
arguments = snipParametersDict['arguments']
stack = self.getStackDataObject()
function(stack, *arguments)
self.setStack(stack)
def subtractActiveCurve(self):
curve = self.getActiveCurve()
if curve is None:
raise ValueError("No active curve")
x, y, legend, info = curve[:4]
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
x0, y0, legend0, info0 = self.getStackOriginalCurve()[:4]
if self.getGraphXLabel().upper() not in ["CHANNEL", "POINTS"]:
# get the used calibration
a, b, c = info.get("McaCalib", [0.0, 1,0, 0.0])
x0 = a + b * x0 + c * x0 * x0
interpolate = True
if x0.size == x.size:
if numpy.allclose(x, x0):
interpolate = False
if interpolate:
xmin = max(x.min(), x0.min())
xmax = min(x.max(), x0.max())
selection = (x0 >= xmin) & (x0 <= xmax)
idx = numpy.nonzero(selection)[0]
if not idx.size:
raise ValueError("Curves do not overlap")
xwork = x0[idx]
# we have got the final x values, interpolate into the
# curve to be subtracted
ywork = numpy.interp(xwork, x, y)
#proceed to subtract the data
notIdx = numpy.nonzero(selection == False)[0]
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
#for i in range(stack.data.shape[-1]):
stack.data[:, :, idx] = stack.data[:, :, idx] - ywork
stack.data[:, :, notIdx] = 0.0
elif mcaIndex == 0:
counter = 0
for i in range(stack.data.shape[0]):
if i in idx:
stack.data[i] -= ywork[counter]
counter += 1
else:
stack.data[i] = 0.0
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
else:
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
for i in range(stack.data.shape[-1]):
stack.data[:, :, i] -= y[i]
elif mcaIndex == 0:
for i in range(stack.data.shape[0]):
stack.data[i] -= y[i]
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
self.setStack(stack)
MENU_TEXT = "Stack Filtering Options"
def getStackPluginInstance(stackWindow, **kw):
ob = BackgroundStackPlugin(stackWindow)
return ob
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